Table 1.
Expression QTL master regulators identified in longissimus dorsi muscle. The SNP location (BTA: bp), SNP name, cluster number from Fig. 1, minor allele frequency, number of eQTLs associated with each master regulator, the proportion of DEG eQTLs, and the harboring or closest gene are shown for each eQTL master regulator
| SNP location | SNP name | Clustera | MAF (%) | Number | % DEG | Harboring gene or closest genes b |
|---|---|---|---|---|---|---|
| of eQTLs | eQTLs | |||||
| 1: 119,758,395 | rs378343630 | 1 | 4 | 62 | 0.0 | TM4SF1 |
| 2: 11,594,176 | rs208227436 | 2 | 3 | 26 | 7.7 | ZNF804A |
| 2: 25,653,736 | rs211476449 | 3 | 3 | 36 | 13.9 | GAD1 |
| 3: 102,943,677 | rs135786834 | 4 | 2 | 32 | 0.0 | KDM4A |
| 5: 27,001,953 | rs441241989 | 5 | 8 | 27 | 18.5 | CSAD |
| 5: 27,834,250 | rs110130901 | 5 | 8 | 25 | 24.0 | KRT7 |
| 5: 105,380,442 | rs207649022 | 6 | 24 | 76 | 69.7 | NTF3 - KCNA5 |
| 7: 92,439,344 | rs110618957 | 7 | 2 | 34 | 8.8 | POLR3G - GPR98 |
| 8: 95,625,807 | ARS_BFGL_N-GS_65636 | 8 | 3 | 111 | 8.1 | ENSBTAG00000047350 - OR13F1 |
| 8: 104,345,143 | rs378706947 | 8 | 2 | 22 | 9.1 | ALAD |
| 10: 8,457,276 | Bovine-HD1000002801 | 9 | 30 | 27 | 74.1 | PDE8B |
| 11: 46,753,639 | rs211218494 | 10 | 8 | 37 | 13.5 | PSD4 |
| 11: 46,785,388 | rs209448226 | 10 | 8 | 37 | 13.5 | 5S_rRNA - PAX8 |
| 13: 54,009,694 | rs135144232 | 11 | 4 | 24 | 8.3 | ENSBTAG00000011638 |
| 14: 74,732,269 | rs208451702 | 12 | 3 | 24 | 8.3 | RUNX1T1 |
| 15: 79,202,054 | rs41781450 | 13 | 37 | 20 | 35.0 | OR4X1 - OR4S1 |
| 15: 79,564,333 | rs109630111 | 13 | 24 | 36 | 2.8 | ENSBTAG00000035487 |
| 16: 62,544,863 | rs456174577 | 14 | 2 | 36 | 0.0 | TOR1AIP1 |
| 17: 30,508,078 | BTB_00676236 | 15 | 41 | 34 | 23.5 | INTU - FAT4 |
| 18: 56,858,212 | rs41891374 | 16 | 5 | 20 | 20.0 | C18H19ORF41 - MYH14 |
| 18: 57,361,426 | rs383445569 | 16 | 4 | 41 | 17.1 | KLK4 |
| 18: 61,257,126 | No SNP name | 17 | 49 | 133 | 2.3 | ENSBTAG00000000336 - ENSBTAG00000046961 |
| 19: 42,754,262 | rs377935001 | 18 | 2 | 34 | 0.0 | TTC25 |
| 22: 16,367,834 | rs110289782 | 19 | 11 | 24 | 50.0 | ENSBTAG00000030533 - ZNF445 |
| 26: 12,930,282 | rs42085062 | 20 | 4 | 23 | 26.1 | PCGF5 |
| 27: 31,921,721 | rs136162903 | 21 | 3 | 25 | 0.0 | KCNU1 |
| 28: 4,877,558 | rs207999887 | 22 | 5 | 34 | 5.9 | SNORA25 - SIPA1L2 |
aCluster number used in Fig. 1
bBolded genes were selected as master regulators when the associated SNP was intergenic; underlined gene names were identified as expressed in skeletal muscle in the present analysis.